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Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions. Hypergraphs are mathematically tractable objects that can be utilized…
The advancement of graph-based malware analysis is critically limited by the absence of large-scale datasets that capture the inherent hierarchical structure of software. Existing methods often oversimplify programs into single level…
In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of…
High throughput screening of compounds (chemicals) is an essential part of drug discovery [7], involving thousands to millions of compounds, with the purpose of identifying candidate hits. Most statistical tools, including the industry…
Motivation: Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution,…
The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next generation genome sequencing methods used in precision medicine…
We present a novel way to encode compositional information in high-dimensional (HD) vectors. Inspired by chromosomal crossover, random HD vectors are recursively interwoven, with a fraction of one vector's components masked out and replaced…
Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated…
In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure,…
Biclustering is an unsupervised machine-learning approach aiming to cluster rows and columns simultaneously in a data matrix. Several biclustering algorithms have been proposed for handling numeric datasets. However, real-world data mining…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…
Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
Revealing relationships between genes and disease phenotypes is a critical problem in biomedical studies. This problem has been challenged by the heterogeneity of diseases. Patients of a perceived same disease may form multiple subgroups,…
Many high dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These…
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
Exploring causal relationships for qualitative data analysis in HCI and social science research enables the understanding of user needs and theory building. However, current computational tools primarily characterize and categorize…
To facilitate the analysis of large-scale high-throughput capillary electrophoresis data, we previously proposed a suite of efficient analysis software named HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis). HiTRACE…